Contacts of the strand formed by residues 89 - 95 (chain A) in PDB entry 1JTE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 6.0 0.4 - - + -
59A LEU* 3.6 32.5 - - + +
61A GLY 5.1 0.2 - - - -
62A ALA 3.4 13.9 - - - +
64A VAL* 3.8 19.7 - - + -
82A PHE* 3.7 34.1 - - + -
87A VAL* 3.6 14.0 + - + +
88A ILE* 1.3 83.4 - - - +
90A LYS* 1.3 82.1 + - - +
91A TRP* 4.0 25.0 + - + +
108A ASP* 3.9 17.8 - - - +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY 6.0 1.8 - - - +
62A ALA 3.2 6.6 + - - +
63A THR* 2.7 40.2 + - + +
64A VAL 2.8 31.4 + - - -
88A ILE* 6.1 3.4 - - + -
89A ILE* 1.3 81.2 - - - +
91A TRP* 1.3 57.9 + - - +
108A ASP* 3.5 11.9 - - + +
128A LEU* 4.6 11.9 + - - +
131A SER* 4.2 14.5 + - - -
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Residues in contact with TRP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.8 10.3 - - + -
63A THR* 4.9 0.4 - - - -
64A VAL* 3.5 37.5 - - + -
66A TYR* 5.2 2.9 - + - -
75A ILE* 4.0 23.6 - - + -
78A LEU* 4.0 30.7 - - + -
79A ARG* 3.7 47.8 + - + +
82A PHE* 4.7 4.2 - + + +
89A ILE* 4.0 33.2 + - + +
90A LYS* 1.3 80.5 - - - +
92A MET* 1.3 60.9 + - - +
93A LEU* 4.0 15.5 - - + -
108A ASP* 2.9 20.9 + - - +
109A VAL* 3.4 14.3 - - + -
110A THR* 3.0 27.8 + - - -
136A ILE* 5.2 5.8 - - + -
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 4.4 10.5 - - + -
64A VAL 2.8 11.9 + - - +
65A VAL* 3.5 6.0 - - - -
66A TYR 2.9 26.2 + - - +
91A TRP* 1.3 74.7 - - - +
93A LEU* 1.3 61.4 + - - +
94A ILE* 3.8 28.5 + - + +
110A THR* 3.5 13.7 - - + +
112A VAL* 4.2 15.0 - - + -
120A TYR* 4.1 9.0 - - - +
124A ILE* 4.4 5.4 - - + -
127A GLN* 3.4 30.1 - - - +
128A LEU* 3.8 33.2 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL 4.8 0.4 - - - +
66A TYR* 3.5 25.8 - - + -
69A SER* 3.4 15.7 - - - +
75A ILE* 4.2 23.6 - - + -
91A TRP* 4.0 23.3 - - + -
92A MET* 1.3 85.3 - - - +
94A ILE* 1.3 54.7 + - - +
99A HIS* 3.8 10.1 - - + +
103A LEU* 4.2 13.5 - - + -
109A VAL* 4.1 12.3 - - + -
110A THR 2.9 10.3 + - - +
111A LEU* 3.5 23.9 - - + -
112A VAL* 2.7 33.1 + - - +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 4.1 20.4 - - + -
66A TYR 2.9 10.6 + - - +
67A ILE* 3.5 7.4 - - + -
68A GLY 2.9 26.2 + - - -
69A SER* 3.3 2.5 + - - -
92A MET* 3.8 32.1 - - + +
93A LEU* 1.3 77.5 - - - +
95A ASP* 1.3 61.6 + - - +
112A VAL* 3.5 27.6 - - + -
114A ARG* 3.4 20.2 - - + +
116A VAL* 3.5 21.5 - - + -
120A TYR* 3.9 15.0 - - + +
124A ILE* 4.3 11.2 - - + -
400A SAH 3.9 1.7 - - - -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLY* 3.2 6.4 - - - -
69A SER 3.1 9.7 + - - -
70A ALA* 2.9 38.1 + - + +
94A ILE* 1.3 76.1 - - - +
96A GLY* 1.3 60.6 + - - +
97A ARG* 2.8 22.2 + - - +
99A HIS* 3.8 7.4 - - + +
112A VAL 2.9 18.7 + - - +
113A THR* 3.0 4.9 - - - -
114A ARG 2.9 16.0 + - - -
400A SAH 2.8 51.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il